Comparative and pangenomic analysis of the genus Streptomyces

Otani, Hiroshi; Udwary, Daniel W.; Mouncey, Nigel J.

doi:10.1038/s41598-022-21731-1

Title: Comparative and pangenomic analysis of the genus Streptomyces

Journal Article · 07 November 2022 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-022-21731-1 · OSTI ID:1897299

Otani, Hiroshi; Udwary, Daniel W.; Mouncey, Nigel J.

Abstract Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1897299

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 12; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis Kittichotirat, Weerayuth; Bumgarner, Roger E.; Asikainen, Sirkka PLoS ONE, Vol. 6, Issue 7 https://doi.org/10.1371/journal.pone.0022420	journal	July 2011
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Comparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species Kim, Ji-Nu; Kim, Yeonbum; Jeong, Yujin Journal of Microbiology and Biotechnology, Vol. 25, Issue 10 https://doi.org/10.4014/jmb.1504.04008	journal	October 2015

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